It sounds like she submitted the new plans in response to a Further Information request (or possibly as unsolicited Further information). If the Further Information is deemed to be significant then the applicant is required to re-advertise (new newspaper & site notices) and there is an additional period for submissions to be made. It sounds like the council have deemed that the resubmitted plans did not constitute significant information and new notices were not required. You could query this but the issue here sounds more like an enforcement issue. If the building is not in compliance with the approved plans then they could be made to take it down.